Natural light environments are highly variable. Flexible adjustment between light energy utilization and photoprotection is therefore of vital importance for plant performance and fitness in the field. Short-term reactions to changing light intensity are triggered inside chloroplasts and leaves within seconds to minutes, whereas long-term adjustments proceed over hours and days, integrating multiple signals. While the mechanisms of long-term acclimation to light intensity have been studied by changing constant growth light intensity during the day, responses to fluctuating growth light intensity have rarely been inspected in detail. We performed transcriptome profiling in Arabidopsis (Arabidopsis thaliana) leaves to investigate long-term gene expression responses to fluctuating light (FL). In particular, we examined whether responses differ between young and mature leaves or between morning and the end of the day. Our results highlight global reprogramming of gene expression under FL, including that of genes related to photoprotection, photosynthesis, and photorespiration and to pigment, prenylquinone, and vitamin metabolism. The FL-induced changes in gene expression varied between young and mature leaves at the same time point and between the same leaves in the morning and at the end of the day, indicating interactions of FL acclimation with leaf development stage and time of day. Only 46 genes were up-or down-regulated in both young and mature leaves at both time points. Combined analyses of gene coexpression and cis-elements pointed to a role of the circadian clock and light in coordinating the acclimatory responses of functionally related genes. Our results also suggest a possible cross talk between FL acclimation and systemic acquired resistance-like gene expression in young leaves.Adjustments of photosynthetic light energy utilization and photoprotection to changing light intensity are triggered over different time scales. Rapid changes (seconds to minutes) are induced inside chloroplasts by reduction of electron transport chain or upon formation of a [H + ] gradient (DpH) across the thylakoid membrane. Short-term responses have been studied intensively to unveil various regulatory mechanisms involved therein. Reduction of the plastoquinone (PQ) pool by preferential excitation of PSII relative to PSI, for example, leads to activation of thylakoid protein kinase STN7, which phosphorylates PSII light-harvesting complex (LHC) to trigger its displacement from PSII to PSI in a process termed state transition (Bellafiore et al., 2005). Light-dependent acidification of thylakoid lumen protonates the PSBS protein to quickly induce thermal energy dissipation (or nonphotochemical quenching [NPQ]) and thus down-regulate PSII (Li et al., 2000). Lumen acidification also activates a xanthophyll-cycle enzyme, violaxanthin deepoxidase (VDE), to convert violaxanthin to antheraxanthin and zeaxanthin, which enhances NPQ (Niyogi et al., 1998). Furthermore, alternative electron (e 2 ) flows (e.g. waterwater cycle and cyclic e 2...